library(sesame)
library(askme)
library(dplyr)
sesame_checkVersion()
## SeSAMe requires matched versions of R, sesame, sesameData and ExperimentHub.
## Here is the current versions installed:
## R: 4.3.0
## Bioconductor: 3.17
## sesame: 1.19.1
## sesameData: 1.19.0
## ExperimentHub: 2.8.0

Classify CNS tumor

pfxes <- searchIDATprefixes("~/repo/askme_test/CapperProsp10_HM450/")[1:2]
betas <- openSesame(pfxes, mask=FALSE)
apply(betas, 2, function(x) askme_cancertype(x, model=m_cancertype_CNS65))
## GSM2940901 GSM2941168 
##  MTGF_ATRT  MTGF_ATRT 
## 65 Levels: ANA PA CHGL CHORDM CN CNS NB, FOXR2 CPH, ADM CPH, PAP ... SUBEPN, ST
betas = openSesame("~/zhou_lab/projects/20230125_nonGEO_IDATs/EPICv2/207107850105_R01C01", collapseToPfx=TRUE, mask=FALSE)
askme_cancertype(betas, model=m_cancertype_CNS65)
##           1 
## MTGF_PLEX_T 
## 65 Levels: ANA PA CHGL CHORDM CN CNS NB, FOXR2 CPH, ADM CPH, PAP ... SUBEPN, ST
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin22.3.0 (64-bit)
## Running under: macOS Ventura 13.2.1
## 
## Matrix products: default
## BLAS:   /Users/zhouw3/.Renv/versions/4.3.0.devel/lib/R/lib/libRblas.dylib 
## LAPACK: /Users/zhouw3/.Renv/versions/4.3.0.devel/lib/R/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] randomForest_4.7-1.1 dplyr_1.1.2          askme_0.99.0        
##  [4] sesame_1.19.1        sesameData_1.19.0    ExperimentHub_2.8.0 
##  [7] AnnotationHub_3.8.0  BiocFileCache_2.8.0  dbplyr_2.3.2        
## [10] BiocGenerics_0.46.0  rmarkdown_2.21       R6_2.5.1            
## 
## loaded via a namespace (and not attached):
##  [1] DBI_1.1.3                     bitops_1.0-7                 
##  [3] rlang_1.1.1                   magrittr_2.0.3               
##  [5] matrixStats_0.63.0            compiler_4.3.0               
##  [7] RSQLite_2.3.1                 png_0.1-8                    
##  [9] vctrs_0.6.2                   reshape2_1.4.4               
## [11] stringr_1.5.0                 pkgconfig_2.0.3              
## [13] crayon_1.5.2                  fastmap_1.1.1                
## [15] XVector_0.40.0                ellipsis_0.3.2               
## [17] utf8_1.2.3                    promises_1.2.0.1             
## [19] tzdb_0.3.0                    preprocessCore_1.62.0        
## [21] purrr_1.0.1                   bit_4.0.5                    
## [23] xfun_0.39                     zlibbioc_1.46.0              
## [25] cachem_1.0.7                  GenomeInfoDb_1.36.0          
## [27] jsonlite_1.8.4                blob_1.2.4                   
## [29] later_1.3.0                   DelayedArray_0.25.0          
## [31] BiocParallel_1.34.0           interactiveDisplayBase_1.38.0
## [33] parallel_4.3.0                bslib_0.4.2                  
## [35] stringi_1.7.12                RColorBrewer_1.1-3           
## [37] GenomicRanges_1.52.0          jquerylib_0.1.4              
## [39] Rcpp_1.0.10                   SummarizedExperiment_1.30.0  
## [41] knitr_1.42                    wheatmap_0.2.0               
## [43] readr_2.1.4                   IRanges_2.34.0               
## [45] httpuv_1.6.9                  illuminaio_0.42.0            
## [47] Matrix_1.5-4                  tidyselect_1.2.0             
## [49] yaml_2.3.7                    codetools_0.2-19             
## [51] curl_5.0.0                    lattice_0.21-8               
## [53] tibble_3.2.1                  plyr_1.8.8                   
## [55] withr_2.5.0                   Biobase_2.60.0               
## [57] shiny_1.7.4                   KEGGREST_1.40.0              
## [59] askpass_1.1                   evaluate_0.20                
## [61] Biostrings_2.68.0             pillar_1.9.0                 
## [63] BiocManager_1.30.20           filelock_1.0.2               
## [65] MatrixGenerics_1.12.0         stats4_4.3.0                 
## [67] generics_0.1.3                RCurl_1.98-1.12              
## [69] BiocVersion_3.17.1            S4Vectors_0.38.0             
## [71] hms_1.1.3                     ggplot2_3.4.2                
## [73] munsell_0.5.0                 scales_1.2.1                 
## [75] BiocStyle_2.27.2              xtable_1.8-4                 
## [77] glue_1.6.2                    tools_4.3.0                  
## [79] grid_4.3.0                    AnnotationDbi_1.62.0         
## [81] colorspace_2.1-0              base64_2.0.1                 
## [83] GenomeInfoDbData_1.2.10       cli_3.6.1                    
## [85] rappdirs_0.3.3                fansi_1.0.4                  
## [87] gtable_0.3.3                  sass_0.4.5                   
## [89] digest_0.6.31                 memoise_2.0.1                
## [91] htmltools_0.5.5               lifecycle_1.0.3              
## [93] httr_1.4.5                    mime_0.12                    
## [95] MASS_7.3-59                   openssl_2.0.6                
## [97] bit64_4.0.5